A method of starting a fuel cell system for a vehicle includes determining whether or not an activation signal of a fuel cell provided in the fuel cell system has been inputted, operating, if it is determined that the activation signal has been inputted, a cooling medium circulation pump to supply a cooling medium to an impurity removal mechanism for reducing a conductivity of the cooling medium, and driving an oxidant gas supply device and a fuel gas supply device in the fuel cell system to start activation of the fuel cell if it is determined that the conductivity of the cooling medium is less than or equal to a predetermined value.